DNA Barcoding Approach to Characterize Microalgae Isolated from Freshwater Systems in Ecuador

The use of suitable DNA barcodes and the generation of databases with reference sequences have been considered a promissory approach for the identification of Chlorophyta and Cyanophyta microalgae. In this study, we carried out a molecular characterization and identification of strains isolated from freshwater systems in Ecuador using a dual barcode method. The target sequences for Chlorophyta were 18S rDNA and rbcL genes, and 16S rDNA and 16S–23S rDNA intergenic spacer (ITS) for Cyanophyta. We reported these DNA barcodes for 20 different Molecular Operational Taxonomic Units (MOTUs) for Chlorophyta and 10 for Cyanophyta. Our results show that the 18S V4 hypervariable region (300 bp) is sufficient for differentiating between isolates, but rbcL is a determinant for genus identification in Scenedesmaceae and Chlorellaceae strains. In Cyanophyta, both barcodes enabled the genus-level assignment of 9 out of 10 MOTUs. These results highlight the necessity of a second barcode additional to small ribosomal subunit sequences to improve molecular identification. Furthermore, the present study significantly contributes to the body of Ecuadorian barcode sequences of microalgae that are currently documented, making them available for future comparative diversity studies.